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Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy

The three-dimensional (3D) genome structure plays a fundamental role in gene regulation and cellular functions. Recent studies in 3D genomics inferred the very basic functional chromatin folding structures known as chromatin loops, the long-range chromatin interactions that are mediated by protein f...

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Autores principales: Parteka-Tojek, Zofia, Zhu, Jacqueline Jufen, Lee, Byoungkoo, Jodkowska, Karolina, Wang, Ping, Aaron, Jesse, Chew, Teng-Leong, Banecki, Krzysztof, Plewczynski, Dariusz, Ruan, Yijun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9122977/
https://www.ncbi.nlm.nih.gov/pubmed/35595799
http://dx.doi.org/10.1038/s41598-022-12568-9
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author Parteka-Tojek, Zofia
Zhu, Jacqueline Jufen
Lee, Byoungkoo
Jodkowska, Karolina
Wang, Ping
Aaron, Jesse
Chew, Teng-Leong
Banecki, Krzysztof
Plewczynski, Dariusz
Ruan, Yijun
author_facet Parteka-Tojek, Zofia
Zhu, Jacqueline Jufen
Lee, Byoungkoo
Jodkowska, Karolina
Wang, Ping
Aaron, Jesse
Chew, Teng-Leong
Banecki, Krzysztof
Plewczynski, Dariusz
Ruan, Yijun
author_sort Parteka-Tojek, Zofia
collection PubMed
description The three-dimensional (3D) genome structure plays a fundamental role in gene regulation and cellular functions. Recent studies in 3D genomics inferred the very basic functional chromatin folding structures known as chromatin loops, the long-range chromatin interactions that are mediated by protein factors and dynamically extruded by cohesin. We combined the use of FISH staining of a very short (33 kb) chromatin fragment, interferometric photoactivated localization microscopy (iPALM), and traveling salesman problem-based heuristic loop reconstruction algorithm from an image of the one of the strongest CTCF-mediated chromatin loops in human lymphoblastoid cells. In total, we have generated thirteen good quality images of the target chromatin region with 2–22 nm oligo probe localization precision. We visualized the shape of the single chromatin loops with unprecedented genomic resolution which allowed us to study the structural heterogeneity of chromatin looping. We were able to compare the physical distance maps from all reconstructed image-driven computational models with contact frequencies observed by ChIA-PET and Hi-C genomic-driven methods to examine the concordance between single cell imaging and population based genomic data.
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spelling pubmed-91229772022-05-22 Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy Parteka-Tojek, Zofia Zhu, Jacqueline Jufen Lee, Byoungkoo Jodkowska, Karolina Wang, Ping Aaron, Jesse Chew, Teng-Leong Banecki, Krzysztof Plewczynski, Dariusz Ruan, Yijun Sci Rep Article The three-dimensional (3D) genome structure plays a fundamental role in gene regulation and cellular functions. Recent studies in 3D genomics inferred the very basic functional chromatin folding structures known as chromatin loops, the long-range chromatin interactions that are mediated by protein factors and dynamically extruded by cohesin. We combined the use of FISH staining of a very short (33 kb) chromatin fragment, interferometric photoactivated localization microscopy (iPALM), and traveling salesman problem-based heuristic loop reconstruction algorithm from an image of the one of the strongest CTCF-mediated chromatin loops in human lymphoblastoid cells. In total, we have generated thirteen good quality images of the target chromatin region with 2–22 nm oligo probe localization precision. We visualized the shape of the single chromatin loops with unprecedented genomic resolution which allowed us to study the structural heterogeneity of chromatin looping. We were able to compare the physical distance maps from all reconstructed image-driven computational models with contact frequencies observed by ChIA-PET and Hi-C genomic-driven methods to examine the concordance between single cell imaging and population based genomic data. Nature Publishing Group UK 2022-05-20 /pmc/articles/PMC9122977/ /pubmed/35595799 http://dx.doi.org/10.1038/s41598-022-12568-9 Text en © The Author(s) 2022, corrected publication 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Parteka-Tojek, Zofia
Zhu, Jacqueline Jufen
Lee, Byoungkoo
Jodkowska, Karolina
Wang, Ping
Aaron, Jesse
Chew, Teng-Leong
Banecki, Krzysztof
Plewczynski, Dariusz
Ruan, Yijun
Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy
title Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy
title_full Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy
title_fullStr Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy
title_full_unstemmed Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy
title_short Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy
title_sort super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9122977/
https://www.ncbi.nlm.nih.gov/pubmed/35595799
http://dx.doi.org/10.1038/s41598-022-12568-9
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